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Report generated at 2020-05-20 09:55:55

Pipeline type: Histone ChIP-Seq

Peak caller: MACS2

Alignment

Flagstat (raw BAM)

	rep1	ctl1
Total	98670962	116197260
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	89830390	114125531
Mapped(QC-failed)	0	0
% Mapped	91.0400	98.2200
Paired	98670962	116197260
Paired(QC-failed)	0	0
Read1	49335481	58098630
Read1(QC-failed)	0	0
Read2	49335481	58098630
Read2(QC-failed)	0	0
Properly Paired	89466193	111936342
Properly Paired(QC-failed)	0	0
% Properly Paired	90.6700	96.3300
With itself	89537723	113460777
With itself(QC-failed)	0	0
Singletons	292667	664754
Singletons(QC-failed)	0	0
% Singleton	0.3000	0.5700
Diff. Chroms	13373	109989
Diff. Chroms (QC-failed)	0	0

Marking duplicates (filtered BAM)

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

	rep1	ctl1
Unpaired Reads	0	0
Paired Reads	42217423	49424273
Unmapped Reads	0	0
Unpaired Dupes	0	0
Paired Dupes	4178145	404585
Paired Opt. Dupes	887	1429
% Dupes/100	0.0990	0.0082

Library complexity (filtered non-mito BAM)

	rep1	ctl1
Total Read Pairs	42216049	49418586
Distinct Read Pairs	38038008	49014360
One Read Pair	34399391	48629916
Two Read Pairs	3244520	376015
NRF = Distinct/Total	0.9010	0.9918
PBC1 = OnePair/Distinct	0.9043	0.9922
PBC2 = OnePair/TwoPair	10.6023	129.3297

Mitochondrial reads are filtered out.

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Flagstat (filtered/deduped BAM)

Filtered and duplicates removed

	rep1	ctl1
Total	76078556	98039376
Total(QC-failed)	0	0
Dupes	0	0
Dupes(QC-failed)	0	0
Mapped	76078556	98039376
Mapped(QC-failed)	0	0
% Mapped	100.0000	100.0000
Paired	76078556	98039376
Paired(QC-failed)	0	0
Read1	38039278	49019688
Read1(QC-failed)	0	0
Read2	38039278	49019688
Read2(QC-failed)	0	0
Properly Paired	76078556	98039376
Properly Paired(QC-failed)	0	0
% Properly Paired	100.0000	100.0000
With itself	76078556	98039376
With itself(QC-failed)	0	0
Singletons	0	0
Singletons(QC-failed)	0	0
% Singleton	0.0000	0.0000
Diff. Chroms	0	0
Diff. Chroms (QC-failed)	0	0

Peak calling

Reproducibility QC and peak detection statistics

The number of peaks is capped at 300K for peak-caller MACS2

	overlap
Nt	0
N1	152366
Np	0
N optimal	152366
N conservative	152366
Optimal Set	rep1-pr
Conservative Set	rep1-pr
Rescue Ratio	0.0000
Self Consistency Ratio	1.0000
Reproducibility	pass

Overlapping peaks

N1: Replicate 1 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Nt: True Replicate consisten overlapping peaks (comparing true replicates Rep1 vs Rep2 )
Np: Pooled-pseudoreplicate consistent overlapping peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2 )
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Enrichment

Strand cross-correlation measures

Performed on subsampled reads (15M)

	rep1
Reads	15000000
Est. Fragment Len.	150
Corr. Est. Fragment Len.	0.2563
Phantom Peak	55
Corr. Phantom Peak	0.2061
Argmin. Corr.	1500
Min. Corr.	0.1803
NSC	1.4215
RSC	2.9523

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Fraction of reads in overlapping peaks

	rep1-pr
Fraction of Reads in Peak	0.6229

ppr: Overlapping peaks comparing pooled pseudo replicates
rep1-pr: Overlapping peaks comparing pseudoreplicates from replicate 1
rep2-pr: Overlapping peaks comparing pseudoreplicates from replicate 2
repi-repj: Overlapping peaks comparing true replicates (rep i vs. rep j)

Other quality metrics

Fingerprint and Jensen-Shannon distance

	rep1
% genome enriched	0.1055
AUC	0.4953
CHANCE divergence	0.2138
Elbow Point	0.0000
JS Distance	0.8411
Synthetic AUC	0.4971
Synthetic Elbow Point	0.4625
Synthetic JS Distance	0.5779